Multiple sequence alignment - TraesCS6B01G337000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6B01G337000 chr6B 100.000 6931 0 0 1 6931 593360065 593353135 0.000000e+00 12800.0
1 TraesCS6B01G337000 chr6A 91.617 5499 328 57 908 6331 543211102 543205662 0.000000e+00 7478.0
2 TraesCS6B01G337000 chr6A 89.518 477 37 7 6412 6875 543205335 543204859 5.990000e-165 592.0
3 TraesCS6B01G337000 chr6A 84.902 457 46 11 464 902 543211589 543211138 2.290000e-119 440.0
4 TraesCS6B01G337000 chr6A 88.393 112 8 5 65 172 543214436 543214326 5.640000e-26 130.0
5 TraesCS6B01G337000 chr6A 94.737 76 4 0 369 444 543211648 543211573 1.220000e-22 119.0
6 TraesCS6B01G337000 chr6D 93.152 4074 210 37 2900 6931 396842531 396838485 0.000000e+00 5914.0
7 TraesCS6B01G337000 chr6D 90.293 2287 152 28 674 2913 396846411 396844148 0.000000e+00 2929.0
8 TraesCS6B01G337000 chr6D 92.975 484 12 5 213 690 396846894 396846427 0.000000e+00 686.0
9 TraesCS6B01G337000 chr6D 100.000 48 0 0 1 48 396915808 396915761 9.580000e-14 89.8
10 TraesCS6B01G337000 chr6D 97.143 35 0 1 65 99 396915776 396915743 2.700000e-04 58.4
11 TraesCS6B01G337000 chr2B 73.669 1033 190 52 3497 4466 57780954 57779941 6.700000e-85 326.0
12 TraesCS6B01G337000 chr2B 77.652 528 84 22 1227 1735 57781625 57781113 2.450000e-74 291.0
13 TraesCS6B01G337000 chr2B 88.732 142 13 2 1227 1368 57682666 57682528 3.320000e-38 171.0
14 TraesCS6B01G337000 chr2B 78.636 220 45 2 5725 5943 57679795 57679577 2.010000e-30 145.0
15 TraesCS6B01G337000 chr2B 77.056 231 37 13 5735 5964 57778786 57778571 1.220000e-22 119.0
16 TraesCS6B01G337000 chr7A 78.947 475 77 20 4847 5310 8750284 8749822 1.130000e-77 302.0
17 TraesCS6B01G337000 chr7A 73.659 634 110 32 3870 4463 8751210 8750594 7.090000e-45 193.0
18 TraesCS6B01G337000 chr4A 78.416 505 75 20 1786 2284 424362204 424362680 1.460000e-76 298.0
19 TraesCS6B01G337000 chr4A 77.778 477 73 27 4847 5310 731421451 731421907 5.330000e-66 263.0
20 TraesCS6B01G337000 chr7D 78.270 474 77 21 4847 5310 8292637 8292180 1.470000e-71 281.0
21 TraesCS6B01G337000 chr7D 73.708 677 127 33 3699 4336 8293728 8293064 4.210000e-52 217.0
22 TraesCS6B01G337000 chr7D 83.838 99 16 0 5735 5833 8291818 8291720 2.060000e-15 95.3
23 TraesCS6B01G337000 chr2A 78.753 433 64 23 1227 1641 38324850 38324428 1.480000e-66 265.0
24 TraesCS6B01G337000 chr2A 90.141 142 11 2 1227 1368 38332750 38332612 1.540000e-41 182.0
25 TraesCS6B01G337000 chr2A 78.947 228 45 3 5723 5948 38321883 38321657 1.200000e-32 152.0
26 TraesCS6B01G337000 chr2A 77.922 231 35 13 5735 5964 38329925 38329710 5.640000e-26 130.0
27 TraesCS6B01G337000 chr2D 75.455 660 91 37 3861 4466 35002212 35001570 8.920000e-64 255.0
28 TraesCS6B01G337000 chr2D 78.729 409 61 15 1233 1629 35025735 35025341 4.150000e-62 250.0
29 TraesCS6B01G337000 chr2D 90.141 142 11 2 1227 1368 35003279 35003141 1.540000e-41 182.0
30 TraesCS6B01G337000 chr2D 79.039 229 44 4 5723 5948 35000411 35000184 3.350000e-33 154.0
31 TraesCS6B01G337000 chr5B 73.767 507 99 25 1787 2285 180910700 180911180 1.200000e-37 169.0
32 TraesCS6B01G337000 chr5B 73.351 379 72 17 1806 2173 690896239 690896599 5.680000e-21 113.0
33 TraesCS6B01G337000 chr5B 92.157 51 3 1 6838 6887 397035986 397036036 3.470000e-08 71.3
34 TraesCS6B01G337000 chr5B 93.478 46 3 0 6838 6883 173366929 173366884 1.250000e-07 69.4
35 TraesCS6B01G337000 chr5B 97.368 38 1 0 2246 2283 369477750 369477787 1.610000e-06 65.8
36 TraesCS6B01G337000 chr7B 88.542 96 9 2 1794 1888 747457390 747457484 1.580000e-21 115.0
37 TraesCS6B01G337000 chr7B 95.556 45 2 0 6839 6883 671910309 671910353 9.640000e-09 73.1
38 TraesCS6B01G337000 chr7B 93.478 46 3 0 6838 6883 224258593 224258548 1.250000e-07 69.4
39 TraesCS6B01G337000 chr4B 93.478 46 3 0 6838 6883 122896444 122896399 1.250000e-07 69.4
40 TraesCS6B01G337000 chr1A 93.478 46 3 0 6838 6883 183488123 183488168 1.250000e-07 69.4
41 TraesCS6B01G337000 chr1A 93.478 46 3 0 6838 6883 574027783 574027738 1.250000e-07 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G337000 chr6B 593353135 593360065 6930 True 12800.000000 12800 100.000000 1 6931 1 chr6B.!!$R1 6930
1 TraesCS6B01G337000 chr6A 543204859 543214436 9577 True 1751.800000 7478 89.833400 65 6875 5 chr6A.!!$R1 6810
2 TraesCS6B01G337000 chr6D 396838485 396846894 8409 True 3176.333333 5914 92.140000 213 6931 3 chr6D.!!$R1 6718
3 TraesCS6B01G337000 chr2B 57778571 57781625 3054 True 245.333333 326 76.125667 1227 5964 3 chr2B.!!$R2 4737
4 TraesCS6B01G337000 chr7A 8749822 8751210 1388 True 247.500000 302 76.303000 3870 5310 2 chr7A.!!$R1 1440
5 TraesCS6B01G337000 chr2A 38321657 38324850 3193 True 208.500000 265 78.850000 1227 5948 2 chr2A.!!$R1 4721

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
34 35 0.179073 GCTCATGCGTGGTCCTGTAT 60.179 55.000 5.98 0.0 0.00 2.29 F
208 340 0.393537 CCTTCCAAGCAATCTCGGCT 60.394 55.000 0.00 0.0 45.15 5.52 F
1160 3747 0.250513 AGTCGATCAAGAACTGGCCC 59.749 55.000 0.00 0.0 0.00 5.80 F
2072 4706 0.456628 TTGACGACACAAGGACGACA 59.543 50.000 0.00 0.0 0.00 4.35 F
3198 7492 0.109153 TGGATCCGCCCATGAATGAG 59.891 55.000 7.39 0.0 34.97 2.90 F
3591 7910 1.195448 ACTCATTTTGTTCTCAGCGCG 59.805 47.619 0.00 0.0 0.00 6.86 F
3611 7930 4.916249 CGCGTCTACCATTATTCTAGGAAC 59.084 45.833 0.00 0.0 0.00 3.62 F
3841 8190 5.698741 TGTGTCCACTATTTCCTGATGAT 57.301 39.130 0.00 0.0 0.00 2.45 F
4992 9529 0.965439 TTTGGTTCCATCGGCCAAAG 59.035 50.000 2.24 0.0 44.41 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1157 3743 0.319405 ATGAACAAGCAAGCAAGGGC 59.681 50.000 0.00 0.00 41.61 5.19 R
1888 4519 1.661480 CTGGTGTCGGTGTCGGTTA 59.339 57.895 0.00 0.00 36.95 2.85 R
2653 5287 0.549950 CTCTGGGGATGATGGCAGTT 59.450 55.000 0.00 0.00 0.00 3.16 R
3230 7524 1.469335 GGTGAACCAGACTCCCACGA 61.469 60.000 0.00 0.00 35.64 4.35 R
4749 9276 2.028748 GGTGTACTTTGGCGAAGTCCTA 60.029 50.000 23.05 8.58 45.40 2.94 R
4896 9433 2.084546 GCAACCTCGTAAGCCAATTCT 58.915 47.619 0.00 0.00 37.18 2.40 R
4992 9529 3.383185 TGTGGATCAACAAAAGGACCAAC 59.617 43.478 0.00 0.00 0.00 3.77 R
5774 10329 0.249868 TGACAAGGCCTTCAGTCACG 60.250 55.000 26.72 13.45 36.20 4.35 R
6836 11650 0.037046 GGCTTGTTGATTTGGCCAGG 60.037 55.000 5.11 0.00 42.08 4.45 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.598257 GTAGACCGTGCATGTGCT 57.402 55.556 4.96 4.20 42.66 4.40
18 19 2.373938 GTAGACCGTGCATGTGCTC 58.626 57.895 4.96 1.75 42.66 4.26
19 20 0.389817 GTAGACCGTGCATGTGCTCA 60.390 55.000 4.96 0.00 42.66 4.26
20 21 0.536724 TAGACCGTGCATGTGCTCAT 59.463 50.000 4.96 0.00 42.66 2.90
27 28 3.582148 CATGTGCTCATGCGTGGT 58.418 55.556 15.22 0.00 43.66 4.16
28 29 1.426621 CATGTGCTCATGCGTGGTC 59.573 57.895 15.22 0.00 43.66 4.02
29 30 1.746615 ATGTGCTCATGCGTGGTCC 60.747 57.895 5.98 0.00 43.34 4.46
30 31 2.046892 GTGCTCATGCGTGGTCCT 60.047 61.111 5.98 0.00 43.34 3.85
31 32 2.046988 TGCTCATGCGTGGTCCTG 60.047 61.111 5.98 0.00 43.34 3.86
32 33 2.046892 GCTCATGCGTGGTCCTGT 60.047 61.111 5.98 0.00 0.00 4.00
33 34 1.218047 GCTCATGCGTGGTCCTGTA 59.782 57.895 5.98 0.00 0.00 2.74
34 35 0.179073 GCTCATGCGTGGTCCTGTAT 60.179 55.000 5.98 0.00 0.00 2.29
35 36 1.858091 CTCATGCGTGGTCCTGTATC 58.142 55.000 5.98 0.00 0.00 2.24
36 37 0.464036 TCATGCGTGGTCCTGTATCC 59.536 55.000 5.98 0.00 0.00 2.59
37 38 0.532862 CATGCGTGGTCCTGTATCCC 60.533 60.000 0.00 0.00 0.00 3.85
38 39 2.028125 ATGCGTGGTCCTGTATCCCG 62.028 60.000 0.00 0.00 0.00 5.14
39 40 2.718073 GCGTGGTCCTGTATCCCGT 61.718 63.158 0.00 0.00 0.00 5.28
40 41 1.386525 GCGTGGTCCTGTATCCCGTA 61.387 60.000 0.00 0.00 0.00 4.02
41 42 1.325355 CGTGGTCCTGTATCCCGTAT 58.675 55.000 0.00 0.00 0.00 3.06
42 43 1.268899 CGTGGTCCTGTATCCCGTATC 59.731 57.143 0.00 0.00 0.00 2.24
43 44 2.313317 GTGGTCCTGTATCCCGTATCA 58.687 52.381 0.00 0.00 0.00 2.15
44 45 2.696707 GTGGTCCTGTATCCCGTATCAA 59.303 50.000 0.00 0.00 0.00 2.57
45 46 2.963101 TGGTCCTGTATCCCGTATCAAG 59.037 50.000 0.00 0.00 0.00 3.02
46 47 2.963782 GGTCCTGTATCCCGTATCAAGT 59.036 50.000 0.00 0.00 0.00 3.16
47 48 3.387050 GGTCCTGTATCCCGTATCAAGTT 59.613 47.826 0.00 0.00 0.00 2.66
48 49 4.141779 GGTCCTGTATCCCGTATCAAGTTT 60.142 45.833 0.00 0.00 0.00 2.66
49 50 5.425630 GTCCTGTATCCCGTATCAAGTTTT 58.574 41.667 0.00 0.00 0.00 2.43
50 51 5.878669 GTCCTGTATCCCGTATCAAGTTTTT 59.121 40.000 0.00 0.00 0.00 1.94
94 95 3.202097 TCAAGTTGATGCGTTTGTCTCA 58.798 40.909 0.08 0.00 0.00 3.27
95 96 3.002246 TCAAGTTGATGCGTTTGTCTCAC 59.998 43.478 0.08 0.00 0.00 3.51
97 98 3.206150 AGTTGATGCGTTTGTCTCACTT 58.794 40.909 0.00 0.00 0.00 3.16
98 99 3.248602 AGTTGATGCGTTTGTCTCACTTC 59.751 43.478 0.00 0.00 0.00 3.01
99 100 3.111853 TGATGCGTTTGTCTCACTTCT 57.888 42.857 0.00 0.00 0.00 2.85
105 109 3.305064 GCGTTTGTCTCACTTCTCTCTCT 60.305 47.826 0.00 0.00 0.00 3.10
106 110 4.472286 CGTTTGTCTCACTTCTCTCTCTC 58.528 47.826 0.00 0.00 0.00 3.20
107 111 4.215399 CGTTTGTCTCACTTCTCTCTCTCT 59.785 45.833 0.00 0.00 0.00 3.10
172 176 5.747197 GCCATTTCTGTGCTCATTTAATCTG 59.253 40.000 0.00 0.00 0.00 2.90
176 308 3.054139 TCTGTGCTCATTTAATCTGGGCT 60.054 43.478 10.69 0.00 40.86 5.19
206 338 0.677731 TGCCTTCCAAGCAATCTCGG 60.678 55.000 0.00 0.00 37.28 4.63
208 340 0.393537 CCTTCCAAGCAATCTCGGCT 60.394 55.000 0.00 0.00 45.15 5.52
209 341 1.134401 CCTTCCAAGCAATCTCGGCTA 60.134 52.381 0.00 0.00 41.66 3.93
222 367 1.218316 CGGCTACCTCACAACCTCC 59.782 63.158 0.00 0.00 0.00 4.30
239 384 2.096496 CCTCCGTGAAATGCAAGATGTC 59.904 50.000 0.00 0.00 0.00 3.06
248 393 1.909700 TGCAAGATGTCCCAGAAACC 58.090 50.000 0.00 0.00 0.00 3.27
358 2673 0.534427 CCTGGATGTCGCATGCTCAT 60.534 55.000 17.13 18.80 0.00 2.90
360 2675 0.877213 TGGATGTCGCATGCTCATCG 60.877 55.000 28.87 12.85 38.86 3.84
479 2975 0.545071 AAAAACCCAGCCCCATGAGG 60.545 55.000 0.00 0.00 0.00 3.86
692 3228 6.317642 TGAAATAATGCACGGTAATGCTAACT 59.682 34.615 0.00 0.00 46.28 2.24
721 3257 1.873698 TCGTTGAAAAGGAACCCTCG 58.126 50.000 0.00 0.00 37.84 4.63
722 3258 1.413445 TCGTTGAAAAGGAACCCTCGA 59.587 47.619 0.00 0.00 37.84 4.04
734 3277 2.721167 CCCTCGATGAACGCCCTCA 61.721 63.158 0.00 0.00 42.26 3.86
744 3287 2.044806 AACGCCCTCACAGCTGTTCT 62.045 55.000 18.94 0.00 0.00 3.01
766 3312 1.066502 TCGAGATCAAACGGCATTGGA 60.067 47.619 0.00 0.00 0.00 3.53
912 3492 3.119096 GACGGCCAGCCTCGAAAC 61.119 66.667 2.24 0.00 0.00 2.78
958 3538 4.080356 CAGACCAAATCCCATAGGTGAAGA 60.080 45.833 0.00 0.00 33.77 2.87
959 3539 4.540099 AGACCAAATCCCATAGGTGAAGAA 59.460 41.667 0.00 0.00 33.77 2.52
960 3540 4.860022 ACCAAATCCCATAGGTGAAGAAG 58.140 43.478 0.00 0.00 32.04 2.85
1011 3597 0.817654 CAGAGACCATGGACTGCGTA 59.182 55.000 21.77 0.00 0.00 4.42
1012 3598 0.818296 AGAGACCATGGACTGCGTAC 59.182 55.000 21.77 6.61 0.00 3.67
1013 3599 0.818296 GAGACCATGGACTGCGTACT 59.182 55.000 21.77 5.50 0.00 2.73
1040 3626 2.608623 AGTGTTTGGAAAATGGGGAGG 58.391 47.619 0.00 0.00 0.00 4.30
1066 3652 5.456497 CACATTGTAATCATCGTTGCCATTC 59.544 40.000 0.00 0.00 0.00 2.67
1089 3675 8.511604 TTCTCTTCATCTTGTTTTCTTGAACT 57.488 30.769 0.00 0.00 0.00 3.01
1100 3686 6.516718 TGTTTTCTTGAACTGTGTTTTGGAA 58.483 32.000 0.00 0.00 0.00 3.53
1156 3742 7.169982 GGACCATTATAAGTCGATCAAGAACTG 59.830 40.741 0.00 0.00 33.66 3.16
1157 3743 6.986817 ACCATTATAAGTCGATCAAGAACTGG 59.013 38.462 0.00 0.00 0.00 4.00
1160 3747 0.250513 AGTCGATCAAGAACTGGCCC 59.749 55.000 0.00 0.00 0.00 5.80
1201 3788 7.833786 TGTCGTTGAGGAATACTAACAGTAAT 58.166 34.615 0.00 0.00 33.89 1.89
1202 3789 8.959548 TGTCGTTGAGGAATACTAACAGTAATA 58.040 33.333 0.00 0.00 33.89 0.98
1203 3790 9.793252 GTCGTTGAGGAATACTAACAGTAATAA 57.207 33.333 0.00 0.00 33.89 1.40
1377 3968 2.710096 AGGCAAGGTATACATGCGTT 57.290 45.000 20.18 12.05 40.94 4.84
1378 3969 3.830744 AGGCAAGGTATACATGCGTTA 57.169 42.857 20.18 0.00 40.94 3.18
1380 3971 2.220133 GGCAAGGTATACATGCGTTACG 59.780 50.000 20.18 0.00 40.94 3.18
1381 3972 2.861935 GCAAGGTATACATGCGTTACGT 59.138 45.455 14.66 0.00 0.00 3.57
1382 3973 4.043750 GCAAGGTATACATGCGTTACGTA 58.956 43.478 14.66 1.27 0.00 3.57
1412 4025 6.518208 AGCTACTATGTCGTCTTCTTTCTT 57.482 37.500 0.00 0.00 0.00 2.52
1423 4036 7.010183 TGTCGTCTTCTTTCTTAACTGTTTCTG 59.990 37.037 0.00 0.00 0.00 3.02
1476 4093 2.040939 CAGAGGATGATGAGGAGCAGT 58.959 52.381 0.00 0.00 0.00 4.40
1491 4108 1.482593 AGCAGTAAGAAGCCGCTGTAT 59.517 47.619 0.00 0.00 0.00 2.29
1626 4243 4.689549 ATGCTGCCCTGCAAGCCA 62.690 61.111 5.68 0.00 46.61 4.75
1848 4479 6.645003 TGTAGCATGACGGATACAATCATAAC 59.355 38.462 0.00 0.00 39.41 1.89
1858 4489 6.141844 CGGATACAATCATAACGAGTACACAC 59.858 42.308 0.00 0.00 0.00 3.82
1893 4524 6.649436 CATAACTAGAATGCACACATAACCG 58.351 40.000 0.00 0.00 34.62 4.44
1894 4525 4.465632 ACTAGAATGCACACATAACCGA 57.534 40.909 0.00 0.00 34.62 4.69
1895 4526 4.181578 ACTAGAATGCACACATAACCGAC 58.818 43.478 0.00 0.00 34.62 4.79
1915 4546 1.597854 CCGACACCAGCACACACAT 60.598 57.895 0.00 0.00 0.00 3.21
2036 4670 3.373748 TGATGATATGCAACAACGACCAC 59.626 43.478 0.00 0.00 0.00 4.16
2058 4692 2.671177 CGCCAACCAGCTCTTGACG 61.671 63.158 2.68 0.00 0.00 4.35
2069 4703 1.409412 CTCTTGACGACACAAGGACG 58.591 55.000 16.43 0.00 44.84 4.79
2072 4706 0.456628 TTGACGACACAAGGACGACA 59.543 50.000 0.00 0.00 0.00 4.35
2140 4774 3.195698 GCCGTCGTTGCCAGATCC 61.196 66.667 0.00 0.00 0.00 3.36
2160 4794 3.055591 CCAACCATCGAAGATCAGATCG 58.944 50.000 4.67 8.70 45.12 3.69
2174 4808 2.901192 TCAGATCGTAGGTTTTCACCCA 59.099 45.455 0.00 0.00 45.63 4.51
2184 4818 5.276461 AGGTTTTCACCCAAAAGATCAAC 57.724 39.130 0.00 0.00 45.63 3.18
2228 4862 2.932614 CCCTCGACAAGCTAACAATCTG 59.067 50.000 0.00 0.00 0.00 2.90
2239 4873 1.878953 AACAATCTGAAGACGCCGTT 58.121 45.000 0.00 0.00 0.00 4.44
2243 4877 4.000988 ACAATCTGAAGACGCCGTTATTT 58.999 39.130 0.00 0.00 0.00 1.40
2292 4926 1.066752 GGTTTTCACCCGGTGCAAC 59.933 57.895 13.19 16.19 37.03 4.17
2347 4981 3.611674 TGAGTCCAGCACCGCGAA 61.612 61.111 8.23 0.00 0.00 4.70
2383 5017 4.021925 GCCACGCAGGGGAAGAGT 62.022 66.667 0.75 0.00 38.09 3.24
2401 5035 3.006537 AGAGTACGCCATACAACACAAGT 59.993 43.478 0.00 0.00 36.09 3.16
2492 5126 3.170672 CCCCCATGAGCCCGATCA 61.171 66.667 0.00 0.00 0.00 2.92
2512 5146 0.541863 ACACCATAGTAGGCCAGCAC 59.458 55.000 5.01 0.00 0.00 4.40
2520 5154 3.958147 TAGGCCAGCACGAGCAAGC 62.958 63.158 5.01 9.04 45.49 4.01
2535 5169 2.620112 AAGCGCACCACATGTCAGC 61.620 57.895 11.47 0.00 0.00 4.26
2562 5196 2.069776 CCACCTGCTGGAAAGGAGA 58.930 57.895 17.64 0.00 43.95 3.71
2598 5232 1.202533 CGAAGGCCGAACATCACCTAT 60.203 52.381 0.00 0.00 41.76 2.57
2620 5254 2.142761 ACACCTCAGAGCAGCCACA 61.143 57.895 0.00 0.00 0.00 4.17
2636 5270 4.619227 CACCCACCGCCACGAACT 62.619 66.667 0.00 0.00 0.00 3.01
2669 5303 1.307309 CCAACTGCCATCATCCCCA 59.693 57.895 0.00 0.00 0.00 4.96
2722 5356 1.134699 AGCGGCGATGAGATGAGAAAA 60.135 47.619 12.98 0.00 0.00 2.29
2749 5383 1.285950 GGGAAAAGTTGTGGCGCTC 59.714 57.895 7.64 1.21 0.00 5.03
2750 5384 1.082104 GGAAAAGTTGTGGCGCTCG 60.082 57.895 7.64 0.00 0.00 5.03
2793 5448 2.042464 TGAGTGACTTCCAAGACTGCT 58.958 47.619 0.00 0.00 0.00 4.24
2800 5455 2.286872 CTTCCAAGACTGCTGGCTATG 58.713 52.381 0.00 0.69 0.00 2.23
2815 5470 5.551233 CTGGCTATGCTATTAACCTTGCTA 58.449 41.667 0.00 0.00 0.00 3.49
2824 5479 7.944061 TGCTATTAACCTTGCTATTACGAGTA 58.056 34.615 0.00 0.00 0.00 2.59
2848 5503 3.243234 CCATATGCTTCGACTTCTCTCGT 60.243 47.826 0.00 0.00 35.10 4.18
2850 5505 2.051879 TGCTTCGACTTCTCTCGTTG 57.948 50.000 0.00 0.00 35.10 4.10
2865 5520 2.913578 TTGGCTGCCTGGTTGCTG 60.914 61.111 21.03 0.00 0.00 4.41
2868 5523 2.914097 GCTGCCTGGTTGCTGGTT 60.914 61.111 0.00 0.00 0.00 3.67
2890 5545 6.034150 GGTTAGCGGGAACAATTTTAAATTCG 59.966 38.462 0.00 2.53 0.00 3.34
2932 7217 6.051179 AGGTAGGAATTTGGTCTAGTTGAC 57.949 41.667 0.00 0.00 44.63 3.18
2974 7262 4.463539 TCTTTGTAATGGTGCATGCAAGAT 59.536 37.500 24.58 14.36 0.00 2.40
2989 7277 4.910195 TGCAAGATCACAATTACAGGAGT 58.090 39.130 0.00 0.00 0.00 3.85
2994 7282 5.491982 AGATCACAATTACAGGAGTGAACC 58.508 41.667 0.00 0.00 43.38 3.62
3011 7299 7.500559 GGAGTGAACCAGCTGATTAAAAGATAT 59.499 37.037 17.39 0.00 0.00 1.63
3090 7378 2.095718 GCTTTGGACGTTGGAGTGAATC 60.096 50.000 0.00 0.00 0.00 2.52
3092 7380 0.669318 TGGACGTTGGAGTGAATCGC 60.669 55.000 0.00 0.00 0.00 4.58
3148 7436 8.710835 TGGTAAAAAGAAACTTCACATTTTCC 57.289 30.769 0.00 0.00 32.98 3.13
3149 7437 8.536175 TGGTAAAAAGAAACTTCACATTTTCCT 58.464 29.630 0.00 0.00 32.98 3.36
3167 7455 1.136305 CCTAGTGTGATGTGGTACCCG 59.864 57.143 10.07 0.00 0.00 5.28
3172 7460 0.606604 GTGATGTGGTACCCGTGACT 59.393 55.000 10.07 0.00 0.00 3.41
3193 7487 1.121407 CCTACTGGATCCGCCCATGA 61.121 60.000 7.39 0.00 35.33 3.07
3198 7492 0.109153 TGGATCCGCCCATGAATGAG 59.891 55.000 7.39 0.00 34.97 2.90
3202 7496 2.734755 TCCGCCCATGAATGAGATTT 57.265 45.000 0.00 0.00 0.00 2.17
3207 7501 4.279169 CCGCCCATGAATGAGATTTTACAT 59.721 41.667 0.00 0.00 0.00 2.29
3210 7504 6.459985 CGCCCATGAATGAGATTTTACATCAA 60.460 38.462 0.00 0.00 0.00 2.57
3230 7524 7.069085 ACATCAATGAGCTTAAAATGGCACTAT 59.931 33.333 0.00 0.00 0.00 2.12
3265 7559 4.038642 GGTTCACCAACATGTAACCACAAT 59.961 41.667 18.52 0.00 39.51 2.71
3279 7573 7.199766 TGTAACCACAATTCTAAACAAAGCAG 58.800 34.615 0.00 0.00 0.00 4.24
3280 7574 6.463995 AACCACAATTCTAAACAAAGCAGA 57.536 33.333 0.00 0.00 0.00 4.26
3329 7623 9.899226 GTTGATAAATGCTTAGAAATATCCACC 57.101 33.333 0.00 0.00 0.00 4.61
3348 7643 4.412207 CACCGCAAAAGGCTTAGAAATAC 58.588 43.478 0.00 0.00 41.67 1.89
3357 7652 4.781934 AGGCTTAGAAATACCGCAAAGAT 58.218 39.130 0.00 0.00 0.00 2.40
3369 7664 8.466086 AATACCGCAAAGATTTCAGAAAATTC 57.534 30.769 0.00 0.00 35.21 2.17
3372 7667 5.695816 CCGCAAAGATTTCAGAAAATTCCAA 59.304 36.000 0.00 0.00 35.21 3.53
3467 7781 7.671398 CCATCTTTAACAGATTGGCCCTTATAT 59.329 37.037 0.00 0.00 40.67 0.86
3588 7907 3.364366 CGGTCACTCATTTTGTTCTCAGC 60.364 47.826 0.00 0.00 0.00 4.26
3591 7910 1.195448 ACTCATTTTGTTCTCAGCGCG 59.805 47.619 0.00 0.00 0.00 6.86
3611 7930 4.916249 CGCGTCTACCATTATTCTAGGAAC 59.084 45.833 0.00 0.00 0.00 3.62
3808 8156 9.750125 AATGATAACTTCACCTTTGTTTTTCTC 57.250 29.630 0.00 0.00 37.11 2.87
3836 8185 7.174946 ACATAAAGTTGTGTCCACTATTTCCTG 59.825 37.037 0.00 0.09 0.00 3.86
3841 8190 5.698741 TGTGTCCACTATTTCCTGATGAT 57.301 39.130 0.00 0.00 0.00 2.45
4642 9152 9.537848 GTTAGTTCCATTCATTGTAAGTAAACG 57.462 33.333 0.00 0.00 0.00 3.60
4798 9325 6.811170 CCTTTACAGTGAACACAATTGTTGTT 59.189 34.615 19.56 19.56 46.43 2.83
4992 9529 0.965439 TTTGGTTCCATCGGCCAAAG 59.035 50.000 2.24 0.00 44.41 2.77
5166 9711 5.110940 AGACTATAAGTTTCCGATCGAGC 57.889 43.478 18.66 0.00 0.00 5.03
5175 9722 1.996292 TCCGATCGAGCTTGTTCTTG 58.004 50.000 18.66 0.00 0.00 3.02
5310 9858 6.710597 ATAGCTCGAGTTGTCATAAGGTAA 57.289 37.500 15.13 0.00 0.00 2.85
5708 10262 5.428253 TGCCCTCAATCTCTATGTTTACAC 58.572 41.667 0.00 0.00 0.00 2.90
5821 10376 1.066858 TGAAAAGGCTAGGAGACGCAG 60.067 52.381 0.00 0.00 0.00 5.18
5823 10378 0.820871 AAAGGCTAGGAGACGCAGAG 59.179 55.000 0.00 0.00 0.00 3.35
5836 10391 1.482593 ACGCAGAGGAATCCCAAGTAG 59.517 52.381 0.00 0.00 33.88 2.57
5881 10436 1.881973 GCAAGTTGATGAGGCAAGTGA 59.118 47.619 7.16 0.00 32.07 3.41
5925 10480 2.429478 CACATGCAGACTCATTGGTGA 58.571 47.619 0.00 0.00 0.00 4.02
5949 10504 7.125204 TGAAGTAAAGGACTGCTAGGCTAATTA 59.875 37.037 0.00 0.00 38.87 1.40
6137 10692 8.072567 GGATCTACACATGTGAAAATGATAAGC 58.927 37.037 31.94 13.40 0.00 3.09
6204 10759 0.393077 CCAACTATGGTCTAGGGGCG 59.607 60.000 0.00 0.00 42.18 6.13
6205 10760 0.393077 CAACTATGGTCTAGGGGCGG 59.607 60.000 0.00 0.00 0.00 6.13
6206 10761 0.763223 AACTATGGTCTAGGGGCGGG 60.763 60.000 0.00 0.00 0.00 6.13
6207 10762 1.913762 CTATGGTCTAGGGGCGGGG 60.914 68.421 0.00 0.00 0.00 5.73
6208 10763 3.477956 TATGGTCTAGGGGCGGGGG 62.478 68.421 0.00 0.00 0.00 5.40
6243 10798 7.103641 TCTTATCGCAAATTTCTACTTCCAGT 58.896 34.615 0.00 0.00 0.00 4.00
6250 10805 9.834628 CGCAAATTTCTACTTCCAGTTTTAATA 57.165 29.630 0.00 0.00 0.00 0.98
6272 10827 2.653726 TGGCAGTTTTGAGAGCAAGAA 58.346 42.857 0.00 0.00 35.04 2.52
6276 10831 4.440663 GGCAGTTTTGAGAGCAAGAAAACT 60.441 41.667 0.00 0.00 46.08 2.66
6289 10844 8.200792 AGAGCAAGAAAACTAGGACTATACATG 58.799 37.037 0.00 0.00 0.00 3.21
6331 10886 5.546621 AGTTAACAAGAGTACCAAGAGCA 57.453 39.130 8.61 0.00 0.00 4.26
6350 10905 7.138692 AGAGCAAAGAATAACAACTAGCAAG 57.861 36.000 0.00 0.00 0.00 4.01
6387 10951 4.082733 GGGGTAAAGAGAATGCAAACACTC 60.083 45.833 0.00 0.00 0.00 3.51
6401 10966 3.818961 AACACTCGTGATGCAAGAATG 57.181 42.857 3.74 0.00 0.00 2.67
6443 11244 3.454812 AGTTGGCAATATCCTAAGTCCGT 59.545 43.478 1.92 0.00 0.00 4.69
6444 11245 3.469008 TGGCAATATCCTAAGTCCGTG 57.531 47.619 0.00 0.00 0.00 4.94
6482 11283 9.720769 TTCAAAATAAAGGTTCTAGGAGTACAG 57.279 33.333 0.00 0.00 0.00 2.74
6484 11285 6.809976 AATAAAGGTTCTAGGAGTACAGGG 57.190 41.667 0.00 0.00 0.00 4.45
6499 11300 0.987294 CAGGGTCCCTTGTGTCATCT 59.013 55.000 8.08 0.00 0.00 2.90
6505 11306 3.054361 GGTCCCTTGTGTCATCTACCAAT 60.054 47.826 0.00 0.00 0.00 3.16
6514 11315 4.572389 GTGTCATCTACCAATCATGTCACC 59.428 45.833 0.00 0.00 33.25 4.02
6531 11345 3.056891 GTCACCCACCAATTATGTTGTGG 60.057 47.826 0.00 0.00 38.46 4.17
6534 11348 2.178580 CCACCAATTATGTTGTGGGCT 58.821 47.619 0.00 0.00 36.69 5.19
6535 11349 2.094078 CCACCAATTATGTTGTGGGCTG 60.094 50.000 0.00 0.00 36.69 4.85
6539 11353 0.336048 ATTATGTTGTGGGCTGGCCT 59.664 50.000 21.72 2.06 36.10 5.19
6657 11471 5.305585 ACAATAGCGAGGAAGTTGAAAAGA 58.694 37.500 0.00 0.00 0.00 2.52
6673 11487 6.922980 TGAAAAGACGAACTTAGTACATCG 57.077 37.500 3.74 3.74 37.93 3.84
6689 11503 4.273148 ACATCGGCCCTAGACATTATTC 57.727 45.455 0.00 0.00 0.00 1.75
6706 11520 7.051623 ACATTATTCGTACATAAAAGGCCTCA 58.948 34.615 5.23 0.00 0.00 3.86
6721 11535 3.118112 AGGCCTCAATCAGAGTGGTAATG 60.118 47.826 0.00 0.00 43.12 1.90
6759 11573 6.199908 GCATAACAGTAGCAGACTCAATACAG 59.800 42.308 0.00 0.00 35.64 2.74
6764 11578 6.071108 ACAGTAGCAGACTCAATACAGACATT 60.071 38.462 0.00 0.00 35.64 2.71
6770 11584 6.758416 GCAGACTCAATACAGACATTGATACA 59.242 38.462 0.00 0.00 42.49 2.29
6800 11614 4.031691 CACATCGTAGTCATCGAACTCAG 58.968 47.826 0.00 0.00 40.61 3.35
6836 11650 1.186267 ATAGGGATCGTCTTCGGGGC 61.186 60.000 0.00 0.00 37.69 5.80
6868 11682 4.065088 TCAACAAGCCAAGTGAGTACATC 58.935 43.478 0.00 0.00 0.00 3.06
6871 11685 3.244078 ACAAGCCAAGTGAGTACATCGAA 60.244 43.478 0.00 0.00 0.00 3.71
6895 11709 8.528044 AATGTACTCCCAAAAAGACAAACTTA 57.472 30.769 0.00 0.00 37.93 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.389817 TGAGCACATGCACGGTCTAC 60.390 55.000 6.64 0.00 45.16 2.59
1 2 0.536724 ATGAGCACATGCACGGTCTA 59.463 50.000 6.64 1.72 45.16 2.59
2 3 1.022982 CATGAGCACATGCACGGTCT 61.023 55.000 11.27 3.68 45.51 3.85
3 4 1.426621 CATGAGCACATGCACGGTC 59.573 57.895 11.27 0.00 45.51 4.79
4 5 3.582148 CATGAGCACATGCACGGT 58.418 55.556 11.27 0.00 45.51 4.83
11 12 1.746615 GGACCACGCATGAGCACAT 60.747 57.895 0.00 0.00 42.27 3.21
12 13 2.358615 GGACCACGCATGAGCACA 60.359 61.111 0.00 0.00 42.27 4.57
13 14 2.046892 AGGACCACGCATGAGCAC 60.047 61.111 0.00 0.00 42.27 4.40
14 15 1.540435 TACAGGACCACGCATGAGCA 61.540 55.000 0.00 0.00 42.27 4.26
15 16 0.179073 ATACAGGACCACGCATGAGC 60.179 55.000 0.00 0.00 37.42 4.26
16 17 1.539065 GGATACAGGACCACGCATGAG 60.539 57.143 0.00 0.00 0.00 2.90
17 18 0.464036 GGATACAGGACCACGCATGA 59.536 55.000 0.00 0.00 0.00 3.07
18 19 0.532862 GGGATACAGGACCACGCATG 60.533 60.000 0.00 0.00 39.74 4.06
19 20 1.830145 GGGATACAGGACCACGCAT 59.170 57.895 0.00 0.00 39.74 4.73
20 21 2.717044 CGGGATACAGGACCACGCA 61.717 63.158 0.00 0.00 39.74 5.24
21 22 1.386525 TACGGGATACAGGACCACGC 61.387 60.000 0.00 0.00 39.74 5.34
22 23 1.268899 GATACGGGATACAGGACCACG 59.731 57.143 0.00 0.00 39.74 4.94
23 24 2.313317 TGATACGGGATACAGGACCAC 58.687 52.381 0.00 0.00 39.74 4.16
24 25 2.759839 TGATACGGGATACAGGACCA 57.240 50.000 0.00 0.00 39.74 4.02
25 26 2.963782 ACTTGATACGGGATACAGGACC 59.036 50.000 0.00 0.00 39.74 4.46
26 27 4.667519 AACTTGATACGGGATACAGGAC 57.332 45.455 0.00 0.00 39.74 3.85
27 28 5.687166 AAAACTTGATACGGGATACAGGA 57.313 39.130 0.00 0.00 39.74 3.86
52 53 7.827236 ACTTGATACGGGATATTGTCTCAAAAA 59.173 33.333 0.00 0.00 32.88 1.94
53 54 7.335627 ACTTGATACGGGATATTGTCTCAAAA 58.664 34.615 0.00 0.00 32.88 2.44
54 55 6.884832 ACTTGATACGGGATATTGTCTCAAA 58.115 36.000 0.00 0.00 32.88 2.69
55 56 6.479972 ACTTGATACGGGATATTGTCTCAA 57.520 37.500 0.00 5.20 32.48 3.02
56 57 6.097696 TCAACTTGATACGGGATATTGTCTCA 59.902 38.462 0.00 0.00 0.00 3.27
57 58 6.513180 TCAACTTGATACGGGATATTGTCTC 58.487 40.000 0.00 0.00 0.00 3.36
58 59 6.479972 TCAACTTGATACGGGATATTGTCT 57.520 37.500 0.00 0.00 0.00 3.41
59 60 6.347725 GCATCAACTTGATACGGGATATTGTC 60.348 42.308 3.88 0.00 34.28 3.18
60 61 5.470098 GCATCAACTTGATACGGGATATTGT 59.530 40.000 3.88 0.00 34.28 2.71
61 62 5.389830 CGCATCAACTTGATACGGGATATTG 60.390 44.000 14.31 0.00 39.33 1.90
62 63 4.690748 CGCATCAACTTGATACGGGATATT 59.309 41.667 14.31 0.00 39.33 1.28
63 64 4.245660 CGCATCAACTTGATACGGGATAT 58.754 43.478 14.31 0.00 39.33 1.63
172 176 1.332195 AGGCAAAACTCAAGAAGCCC 58.668 50.000 0.00 0.00 42.97 5.19
176 308 3.181476 GCTTGGAAGGCAAAACTCAAGAA 60.181 43.478 0.00 0.00 35.08 2.52
201 333 0.251653 AGGTTGTGAGGTAGCCGAGA 60.252 55.000 0.00 0.00 0.00 4.04
203 335 1.255667 GGAGGTTGTGAGGTAGCCGA 61.256 60.000 0.00 0.00 0.00 5.54
204 336 1.218316 GGAGGTTGTGAGGTAGCCG 59.782 63.158 0.00 0.00 0.00 5.52
206 338 0.389948 CACGGAGGTTGTGAGGTAGC 60.390 60.000 0.00 0.00 39.73 3.58
208 340 1.707106 TTCACGGAGGTTGTGAGGTA 58.293 50.000 0.00 0.00 46.17 3.08
209 341 0.834612 TTTCACGGAGGTTGTGAGGT 59.165 50.000 0.00 0.00 46.17 3.85
222 367 1.811965 TGGGACATCTTGCATTTCACG 59.188 47.619 0.00 0.00 0.00 4.35
239 384 3.256631 CAGGACAAAATCAGGTTTCTGGG 59.743 47.826 0.00 0.00 41.23 4.45
248 393 4.096984 GGATTACAGGCAGGACAAAATCAG 59.903 45.833 0.00 0.00 0.00 2.90
358 2673 4.262292 CCATTTCGGGGATATACAAGTCGA 60.262 45.833 0.00 0.00 0.00 4.20
360 2675 3.751698 GCCATTTCGGGGATATACAAGTC 59.248 47.826 0.00 0.00 34.06 3.01
463 2959 0.849094 TAACCTCATGGGGCTGGGTT 60.849 55.000 13.00 9.84 42.11 4.11
466 2962 1.152881 GCTAACCTCATGGGGCTGG 60.153 63.158 13.00 1.81 40.03 4.85
479 2975 0.804933 CGCCCGTGTCCTTAGCTAAC 60.805 60.000 0.86 0.00 0.00 2.34
721 3257 1.078848 AGCTGTGAGGGCGTTCATC 60.079 57.895 0.00 0.00 34.52 2.92
722 3258 1.376424 CAGCTGTGAGGGCGTTCAT 60.376 57.895 5.25 0.00 34.52 2.57
744 3287 3.130633 CCAATGCCGTTTGATCTCGATA 58.869 45.455 0.00 0.00 0.00 2.92
766 3312 8.421249 TTGATCATCTGGTTTTATTTTCAGGT 57.579 30.769 0.00 0.00 0.00 4.00
958 3538 1.632018 TACGCTATGCCCCCAAGCTT 61.632 55.000 0.00 0.00 34.03 3.74
959 3539 2.070039 TACGCTATGCCCCCAAGCT 61.070 57.895 0.00 0.00 34.03 3.74
960 3540 1.892391 GTACGCTATGCCCCCAAGC 60.892 63.158 0.00 0.00 0.00 4.01
1011 3597 4.799564 TTTTCCAAACACTTTGCAGAGT 57.200 36.364 3.61 3.61 39.31 3.24
1012 3598 4.508861 CCATTTTCCAAACACTTTGCAGAG 59.491 41.667 2.03 2.03 39.31 3.35
1013 3599 4.440880 CCATTTTCCAAACACTTTGCAGA 58.559 39.130 0.00 0.00 39.31 4.26
1040 3626 3.108144 GCAACGATGATTACAATGTGCC 58.892 45.455 0.00 0.00 0.00 5.01
1066 3652 7.642978 CACAGTTCAAGAAAACAAGATGAAGAG 59.357 37.037 0.00 0.00 31.24 2.85
1100 3686 2.975489 CACTAGCATAGGGGAAGTCCAT 59.025 50.000 0.00 0.00 44.97 3.41
1156 3742 1.005748 GAACAAGCAAGCAAGGGCC 60.006 57.895 0.00 0.00 42.56 5.80
1157 3743 0.319405 ATGAACAAGCAAGCAAGGGC 59.681 50.000 0.00 0.00 41.61 5.19
1160 3747 2.287188 ACGACATGAACAAGCAAGCAAG 60.287 45.455 0.00 0.00 0.00 4.01
1201 3788 3.412237 GGTCACTGCTAACCCTTGTTA 57.588 47.619 0.00 0.00 35.87 2.41
1202 3789 2.271944 GGTCACTGCTAACCCTTGTT 57.728 50.000 0.00 0.00 38.52 2.83
1377 3968 5.107722 CGACATAGTAGCTTCATCGTACGTA 60.108 44.000 16.05 2.34 0.00 3.57
1378 3969 4.318618 CGACATAGTAGCTTCATCGTACGT 60.319 45.833 16.05 0.00 0.00 3.57
1380 3971 5.050227 AGACGACATAGTAGCTTCATCGTAC 60.050 44.000 10.36 6.47 41.05 3.67
1381 3972 5.055144 AGACGACATAGTAGCTTCATCGTA 58.945 41.667 10.36 0.00 41.05 3.43
1382 3973 3.878103 AGACGACATAGTAGCTTCATCGT 59.122 43.478 10.23 10.23 43.42 3.73
1384 3975 6.067263 AGAAGACGACATAGTAGCTTCATC 57.933 41.667 0.00 0.00 35.44 2.92
1385 3976 6.458232 AAGAAGACGACATAGTAGCTTCAT 57.542 37.500 0.00 0.00 35.44 2.57
1386 3977 5.899120 AAGAAGACGACATAGTAGCTTCA 57.101 39.130 0.00 0.00 35.44 3.02
1387 3978 6.557110 AGAAAGAAGACGACATAGTAGCTTC 58.443 40.000 0.00 0.00 33.72 3.86
1392 3983 8.790718 ACAGTTAAGAAAGAAGACGACATAGTA 58.209 33.333 0.00 0.00 0.00 1.82
1395 3986 8.882415 AAACAGTTAAGAAAGAAGACGACATA 57.118 30.769 0.00 0.00 0.00 2.29
1397 3988 7.010183 CAGAAACAGTTAAGAAAGAAGACGACA 59.990 37.037 0.00 0.00 0.00 4.35
1412 4025 6.548171 GCAACAGTTAACACAGAAACAGTTA 58.452 36.000 8.61 0.00 34.71 2.24
1423 4036 2.456010 CCCAAACGCAACAGTTAACAC 58.544 47.619 8.61 0.00 33.41 3.32
1476 4093 2.100916 GACCTCATACAGCGGCTTCTTA 59.899 50.000 0.00 0.00 0.00 2.10
1568 4185 4.100084 CGCACAGCCTCCCCATGA 62.100 66.667 0.00 0.00 0.00 3.07
1825 4456 5.861787 CGTTATGATTGTATCCGTCATGCTA 59.138 40.000 0.00 0.00 34.62 3.49
1833 4464 6.141844 GTGTGTACTCGTTATGATTGTATCCG 59.858 42.308 0.00 0.00 0.00 4.18
1858 4489 3.536956 TCTAGTTATGCAAAGACCGGG 57.463 47.619 6.32 0.00 0.00 5.73
1888 4519 1.661480 CTGGTGTCGGTGTCGGTTA 59.339 57.895 0.00 0.00 36.95 2.85
1889 4520 2.420043 CTGGTGTCGGTGTCGGTT 59.580 61.111 0.00 0.00 36.95 4.44
1890 4521 4.295119 GCTGGTGTCGGTGTCGGT 62.295 66.667 0.00 0.00 36.95 4.69
1891 4522 4.293648 TGCTGGTGTCGGTGTCGG 62.294 66.667 0.00 0.00 36.95 4.79
1892 4523 3.036084 GTGCTGGTGTCGGTGTCG 61.036 66.667 0.00 0.00 37.82 4.35
1893 4524 2.108157 TGTGCTGGTGTCGGTGTC 59.892 61.111 0.00 0.00 0.00 3.67
1894 4525 2.203015 GTGTGCTGGTGTCGGTGT 60.203 61.111 0.00 0.00 0.00 4.16
1895 4526 2.203001 TGTGTGCTGGTGTCGGTG 60.203 61.111 0.00 0.00 0.00 4.94
1915 4546 2.954989 TGCTGGTGTTATCTTTTGTGCA 59.045 40.909 0.00 0.00 0.00 4.57
1918 4549 5.507985 GCTCTTTGCTGGTGTTATCTTTTGT 60.508 40.000 0.00 0.00 38.95 2.83
1946 4577 3.099267 AGCATAGCGGTCTTGTATGTC 57.901 47.619 0.00 0.00 0.00 3.06
1947 4578 3.543680 AAGCATAGCGGTCTTGTATGT 57.456 42.857 0.00 0.00 0.00 2.29
1988 4622 7.301068 TCGCTTGTTTGATTGTTTTTGAATT 57.699 28.000 0.00 0.00 0.00 2.17
1989 4623 6.900568 TCGCTTGTTTGATTGTTTTTGAAT 57.099 29.167 0.00 0.00 0.00 2.57
1990 4624 6.900568 ATCGCTTGTTTGATTGTTTTTGAA 57.099 29.167 0.00 0.00 0.00 2.69
1991 4625 6.703857 CAATCGCTTGTTTGATTGTTTTTGA 58.296 32.000 6.75 0.00 44.00 2.69
1992 4626 6.939953 CAATCGCTTGTTTGATTGTTTTTG 57.060 33.333 6.75 0.00 44.00 2.44
2017 4651 2.080693 GGTGGTCGTTGTTGCATATCA 58.919 47.619 0.00 0.00 0.00 2.15
2036 4670 1.898574 AAGAGCTGGTTGGCGTTGG 60.899 57.895 0.00 0.00 37.29 3.77
2058 4692 3.390135 TCTTGATTGTCGTCCTTGTGTC 58.610 45.455 0.00 0.00 0.00 3.67
2069 4703 6.017400 TGCTTCCAAAGAATCTTGATTGTC 57.983 37.500 0.00 0.00 0.00 3.18
2072 4706 5.873164 GCATTGCTTCCAAAGAATCTTGATT 59.127 36.000 0.16 0.00 34.05 2.57
2115 4749 2.468532 CAACGACGGCACTAACGC 59.531 61.111 0.00 0.00 34.00 4.84
2118 4752 1.666553 CTGGCAACGACGGCACTAA 60.667 57.895 0.00 0.00 36.38 2.24
2140 4774 3.711086 ACGATCTGATCTTCGATGGTTG 58.289 45.455 15.16 0.00 38.67 3.77
2160 4794 6.040504 AGTTGATCTTTTGGGTGAAAACCTAC 59.959 38.462 0.00 0.00 30.13 3.18
2174 4808 5.240403 GGAGTTTGCTCAGAGTTGATCTTTT 59.760 40.000 0.00 0.00 43.37 2.27
2184 4818 1.888215 TGCTTGGAGTTTGCTCAGAG 58.112 50.000 0.00 0.00 43.37 3.35
2228 4862 1.664151 CCTGGAAATAACGGCGTCTTC 59.336 52.381 15.17 16.08 0.00 2.87
2239 4873 6.910290 ACCCTAGTTGGTTATACCTGGAAATA 59.090 38.462 0.00 0.00 39.58 1.40
2243 4877 4.357313 ACCCTAGTTGGTTATACCTGGA 57.643 45.455 0.00 0.00 39.58 3.86
2292 4926 2.604991 GGCCTCCTATCCCTCCGG 60.605 72.222 0.00 0.00 0.00 5.14
2318 4952 2.593956 GGACTCACCACCCTCCCAC 61.594 68.421 0.00 0.00 38.79 4.61
2340 4974 4.636435 CCACCCCAACTTCGCGGT 62.636 66.667 6.13 0.00 0.00 5.68
2347 4981 1.916777 CCCGACTACCACCCCAACT 60.917 63.158 0.00 0.00 0.00 3.16
2401 5035 2.667874 TGGCGACAATGCGAGCAA 60.668 55.556 0.57 0.00 37.44 3.91
2474 5108 4.650377 GATCGGGCTCATGGGGGC 62.650 72.222 0.00 0.00 0.00 5.80
2481 5115 1.138859 CTATGGTGTTGATCGGGCTCA 59.861 52.381 0.00 0.00 0.00 4.26
2492 5126 1.065418 GTGCTGGCCTACTATGGTGTT 60.065 52.381 3.32 0.00 0.00 3.32
2512 5146 3.425713 ATGTGGTGCGCTTGCTCG 61.426 61.111 9.73 0.00 40.12 5.03
2520 5154 3.792047 CCGCTGACATGTGGTGCG 61.792 66.667 21.98 21.98 45.22 5.34
2553 5187 1.449601 TCCGCGCAATCTCCTTTCC 60.450 57.895 8.75 0.00 0.00 3.13
2580 5214 1.747206 GCATAGGTGATGTTCGGCCTT 60.747 52.381 0.00 0.00 37.90 4.35
2598 5232 2.745698 CTGCTCTGAGGTGTGGCA 59.254 61.111 6.83 0.00 0.00 4.92
2620 5254 2.918802 TAGTTCGTGGCGGTGGGT 60.919 61.111 0.00 0.00 0.00 4.51
2627 5261 1.810030 CCTTCGGCTAGTTCGTGGC 60.810 63.158 7.33 0.00 0.00 5.01
2653 5287 0.549950 CTCTGGGGATGATGGCAGTT 59.450 55.000 0.00 0.00 0.00 3.16
2695 5329 0.886938 TCTCATCGCCGCTAGAGGAG 60.887 60.000 17.75 13.74 44.89 3.69
2705 5339 2.158900 TCCCTTTTCTCATCTCATCGCC 60.159 50.000 0.00 0.00 0.00 5.54
2722 5356 1.573857 ACAACTTTTCCCCAACTCCCT 59.426 47.619 0.00 0.00 0.00 4.20
2760 5415 0.742505 TCACTCAAACTGACGTCCGT 59.257 50.000 14.12 10.36 0.00 4.69
2764 5419 2.167693 TGGAAGTCACTCAAACTGACGT 59.832 45.455 0.00 0.00 42.52 4.34
2765 5420 2.821546 TGGAAGTCACTCAAACTGACG 58.178 47.619 0.00 0.00 42.52 4.35
2793 5448 4.437682 AGCAAGGTTAATAGCATAGCCA 57.562 40.909 0.00 0.00 0.00 4.75
2800 5455 7.328005 GGTACTCGTAATAGCAAGGTTAATAGC 59.672 40.741 0.00 0.00 0.00 2.97
2815 5470 4.521639 TCGAAGCATATGGGTACTCGTAAT 59.478 41.667 4.56 0.00 0.00 1.89
2824 5479 3.034635 AGAGAAGTCGAAGCATATGGGT 58.965 45.455 4.56 0.00 0.00 4.51
2848 5503 2.913578 CAGCAACCAGGCAGCCAA 60.914 61.111 15.80 0.00 35.83 4.52
2850 5505 4.982701 ACCAGCAACCAGGCAGCC 62.983 66.667 1.84 1.84 35.83 4.85
2865 5520 6.034150 CGAATTTAAAATTGTTCCCGCTAACC 59.966 38.462 0.00 0.00 0.00 2.85
2868 5523 5.183522 ACCGAATTTAAAATTGTTCCCGCTA 59.816 36.000 0.00 0.00 0.00 4.26
2937 7222 8.311109 ACCATTACAAAGAAAAACACAGACTTT 58.689 29.630 0.00 0.00 0.00 2.66
2960 7248 1.618487 TTGTGATCTTGCATGCACCA 58.382 45.000 22.58 13.14 0.00 4.17
2974 7262 4.641396 CTGGTTCACTCCTGTAATTGTGA 58.359 43.478 0.00 0.00 37.62 3.58
2989 7277 8.806429 TTGATATCTTTTAATCAGCTGGTTCA 57.194 30.769 17.29 1.51 33.83 3.18
2994 7282 9.064706 AGTCCATTGATATCTTTTAATCAGCTG 57.935 33.333 7.63 7.63 33.83 4.24
3090 7378 4.447724 ACGTATATGTAGCATTTTCCAGCG 59.552 41.667 0.00 0.00 35.48 5.18
3202 7496 7.035004 GTGCCATTTTAAGCTCATTGATGTAA 58.965 34.615 0.00 0.00 0.00 2.41
3207 7501 6.238456 CGATAGTGCCATTTTAAGCTCATTGA 60.238 38.462 0.00 0.00 0.00 2.57
3210 7504 5.679734 CGATAGTGCCATTTTAAGCTCAT 57.320 39.130 0.00 0.00 0.00 2.90
3230 7524 1.469335 GGTGAACCAGACTCCCACGA 61.469 60.000 0.00 0.00 35.64 4.35
3265 7559 9.731819 CTCGTATATACTCTGCTTTGTTTAGAA 57.268 33.333 11.05 0.00 0.00 2.10
3288 7582 9.162793 GCATTTATCAACATTCAACTATTCTCG 57.837 33.333 0.00 0.00 0.00 4.04
3312 7606 3.552132 TGCGGTGGATATTTCTAAGCA 57.448 42.857 0.00 0.00 0.00 3.91
3348 7643 5.229423 TGGAATTTTCTGAAATCTTTGCGG 58.771 37.500 3.31 0.00 34.44 5.69
3369 7664 8.803799 GTGTTGTGTAGTTTGTAAATTTCTTGG 58.196 33.333 0.00 0.00 0.00 3.61
3372 7667 8.952278 TGAGTGTTGTGTAGTTTGTAAATTTCT 58.048 29.630 0.00 0.00 0.00 2.52
3382 7677 5.163754 GCAGAAGTTGAGTGTTGTGTAGTTT 60.164 40.000 0.00 0.00 0.00 2.66
3477 7791 7.336679 CCCTACATGCGGAATATCAAATGAATA 59.663 37.037 3.31 0.00 0.00 1.75
3588 7907 4.761235 TCCTAGAATAATGGTAGACGCG 57.239 45.455 3.53 3.53 0.00 6.01
3591 7910 6.702282 GCACAGTTCCTAGAATAATGGTAGAC 59.298 42.308 0.00 0.00 0.00 2.59
3847 8196 8.435187 TCATTTCAGGAGCTACATAATGAATCT 58.565 33.333 14.44 0.00 30.23 2.40
3859 8209 4.492494 TGCTTGATCATTTCAGGAGCTA 57.508 40.909 13.01 0.01 38.49 3.32
4373 8825 8.801715 AAGAACAACATGCAAAGTAGTTATTG 57.198 30.769 0.00 0.00 0.00 1.90
4619 9116 7.442969 TCACGTTTACTTACAATGAATGGAACT 59.557 33.333 0.00 0.00 0.00 3.01
4749 9276 2.028748 GGTGTACTTTGGCGAAGTCCTA 60.029 50.000 23.05 8.58 45.40 2.94
4758 9285 3.633065 TGTAAAGGTTGGTGTACTTTGGC 59.367 43.478 0.00 0.00 36.07 4.52
4768 9295 3.958018 TGTGTTCACTGTAAAGGTTGGT 58.042 40.909 4.59 0.00 0.00 3.67
4798 9325 7.276658 TCCTTTATGCACGATCCTTGTTATAA 58.723 34.615 0.00 0.00 0.00 0.98
4896 9433 2.084546 GCAACCTCGTAAGCCAATTCT 58.915 47.619 0.00 0.00 37.18 2.40
4992 9529 3.383185 TGTGGATCAACAAAAGGACCAAC 59.617 43.478 0.00 0.00 0.00 3.77
5166 9711 8.624776 AGAATTGGACTAACTTTCAAGAACAAG 58.375 33.333 0.00 0.00 0.00 3.16
5464 10016 3.565307 AGAAGTTCAAAGGCAATCCACA 58.435 40.909 5.50 0.00 33.74 4.17
5637 10191 5.850557 CCTACATGGTGGCATCAAATTTA 57.149 39.130 3.70 0.00 0.00 1.40
5774 10329 0.249868 TGACAAGGCCTTCAGTCACG 60.250 55.000 26.72 13.45 36.20 4.35
5821 10376 3.519913 AGGTGTTCTACTTGGGATTCCTC 59.480 47.826 2.01 0.00 0.00 3.71
5823 10378 3.610911 CAGGTGTTCTACTTGGGATTCC 58.389 50.000 0.00 0.00 33.08 3.01
5836 10391 1.014564 GCCTACGTCTGCAGGTGTTC 61.015 60.000 15.13 2.65 34.18 3.18
5861 10416 1.881973 TCACTTGCCTCATCAACTTGC 59.118 47.619 0.00 0.00 0.00 4.01
5870 10425 1.241165 CTGCAACATCACTTGCCTCA 58.759 50.000 1.64 0.00 45.13 3.86
5881 10436 6.482641 TGCATTTGTTATTTGAACTGCAACAT 59.517 30.769 0.00 0.00 35.63 2.71
5925 10480 5.959583 ATTAGCCTAGCAGTCCTTTACTT 57.040 39.130 0.00 0.00 35.76 2.24
5949 10504 8.090214 GCAAGAATGGCCATATACAAAATATGT 58.910 33.333 21.15 0.00 46.36 2.29
5965 10520 7.260603 AGAAATTGTAGTATTGCAAGAATGGC 58.739 34.615 4.94 0.00 32.32 4.40
6032 10587 7.546667 CACATCAAGAACCAAAATTATCCAAGG 59.453 37.037 0.00 0.00 0.00 3.61
6033 10588 8.090214 ACACATCAAGAACCAAAATTATCCAAG 58.910 33.333 0.00 0.00 0.00 3.61
6044 10599 4.462508 TGCAAAACACATCAAGAACCAA 57.537 36.364 0.00 0.00 0.00 3.67
6099 10654 9.290483 CACATGTGTAGATCCATATATTACGTC 57.710 37.037 18.03 0.00 0.00 4.34
6137 10692 9.878599 AGACGACAATGTTGTTATCTTTAAAAG 57.121 29.630 7.80 0.00 42.43 2.27
6191 10746 4.900259 CCCCCGCCCCTAGACCAT 62.900 72.222 0.00 0.00 0.00 3.55
6209 10764 6.434340 AGAAATTTGCGATAAGAATATCCCCC 59.566 38.462 0.00 0.00 35.47 5.40
6210 10765 7.454260 AGAAATTTGCGATAAGAATATCCCC 57.546 36.000 0.00 0.00 35.47 4.81
6211 10766 9.220767 AGTAGAAATTTGCGATAAGAATATCCC 57.779 33.333 0.00 0.00 35.47 3.85
6240 10795 9.132521 CTCTCAAAACTGCCAATATTAAAACTG 57.867 33.333 0.00 0.00 0.00 3.16
6243 10798 7.665690 TGCTCTCAAAACTGCCAATATTAAAA 58.334 30.769 0.00 0.00 0.00 1.52
6250 10805 3.225104 TCTTGCTCTCAAAACTGCCAAT 58.775 40.909 0.00 0.00 0.00 3.16
6272 10827 7.195374 TCTTTGGCATGTATAGTCCTAGTTT 57.805 36.000 0.00 0.00 0.00 2.66
6276 10831 6.808321 AGTTCTTTGGCATGTATAGTCCTA 57.192 37.500 0.00 0.00 0.00 2.94
6289 10844 3.243535 ACTTGCTTGCTAAGTTCTTTGGC 60.244 43.478 0.00 0.00 43.03 4.52
6350 10905 5.214293 TCTTTACCCCCATCTCCTACTTAC 58.786 45.833 0.00 0.00 0.00 2.34
6387 10951 3.674753 GGGAAAAACATTCTTGCATCACG 59.325 43.478 0.00 0.00 0.00 4.35
6401 10966 4.070009 ACTATCTGAACCACGGGAAAAAC 58.930 43.478 0.00 0.00 0.00 2.43
6443 11244 5.759506 TTATTTTGAAGCCTTCGTCAACA 57.240 34.783 0.00 0.00 39.70 3.33
6444 11245 5.629435 CCTTTATTTTGAAGCCTTCGTCAAC 59.371 40.000 0.00 0.00 39.70 3.18
6482 11283 1.209747 GGTAGATGACACAAGGGACCC 59.790 57.143 0.59 0.59 0.00 4.46
6484 11285 3.695830 TTGGTAGATGACACAAGGGAC 57.304 47.619 0.00 0.00 0.00 4.46
6499 11300 1.988846 TGGTGGGTGACATGATTGGTA 59.011 47.619 0.00 0.00 0.00 3.25
6505 11306 4.314522 ACATAATTGGTGGGTGACATGA 57.685 40.909 0.00 0.00 0.00 3.07
6514 11315 2.094078 CAGCCCACAACATAATTGGTGG 60.094 50.000 0.00 0.00 45.31 4.61
6531 11345 3.102972 TGATATGATCTCTAGGCCAGCC 58.897 50.000 5.01 0.00 0.00 4.85
6534 11348 3.956848 CCGATGATATGATCTCTAGGCCA 59.043 47.826 5.01 0.00 0.00 5.36
6535 11349 3.320541 CCCGATGATATGATCTCTAGGCC 59.679 52.174 0.00 0.00 0.00 5.19
6539 11353 3.300388 GGGCCCGATGATATGATCTCTA 58.700 50.000 5.69 0.00 0.00 2.43
6657 11471 1.135721 GGGCCGATGTACTAAGTTCGT 59.864 52.381 0.00 0.00 0.00 3.85
6673 11487 4.595762 TGTACGAATAATGTCTAGGGCC 57.404 45.455 0.00 0.00 0.00 5.80
6689 11503 5.116180 TCTGATTGAGGCCTTTTATGTACG 58.884 41.667 6.77 0.00 0.00 3.67
6706 11520 5.760253 CGCTTATTCCATTACCACTCTGATT 59.240 40.000 0.00 0.00 0.00 2.57
6721 11535 3.877508 ACTGTTATGCTTCCGCTTATTCC 59.122 43.478 0.00 0.00 36.97 3.01
6759 11573 5.940192 TGTGTTCCAAGTGTATCAATGTC 57.060 39.130 0.00 0.00 0.00 3.06
6764 11578 4.265904 ACGATGTGTTCCAAGTGTATCA 57.734 40.909 0.00 0.00 0.00 2.15
6770 11584 4.495422 GATGACTACGATGTGTTCCAAGT 58.505 43.478 0.00 0.00 0.00 3.16
6800 11614 2.486191 CCTATGCTTGAGGGGATGTCAC 60.486 54.545 0.00 0.00 0.00 3.67
6836 11650 0.037046 GGCTTGTTGATTTGGCCAGG 60.037 55.000 5.11 0.00 42.08 4.45
6841 11655 3.068590 ACTCACTTGGCTTGTTGATTTGG 59.931 43.478 0.00 0.00 0.00 3.28
6842 11656 4.311816 ACTCACTTGGCTTGTTGATTTG 57.688 40.909 0.00 0.00 0.00 2.32
6848 11662 3.067106 CGATGTACTCACTTGGCTTGTT 58.933 45.455 0.00 0.00 0.00 2.83
6868 11682 5.682943 TTGTCTTTTTGGGAGTACATTCG 57.317 39.130 0.00 0.00 0.00 3.34
6871 11685 7.230712 CCTAAGTTTGTCTTTTTGGGAGTACAT 59.769 37.037 0.00 0.00 37.56 2.29


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.